Post Doc

Dr. Shipra Gupta
Shipra Gupta is a Research Associate at IISER, Pune. Before joining the IISER, she was working as a research associate in Bioinformatics center, University of Pune. She obtained her Ph.D. in Bioinformatics from King George's Medical University, Lucknow, India. Her research interests are in molecular modelling the 3D structures of biomolecular complexes, predicting protein-protein and molecular dynamics simulations.

Research Interests:
Her current focus is on modelling the 3D structures of biomolecular complexes and to check how does protein properties change during molecular dynamics simulations. She has made serveral contributions in her areas of research. She has published over 12 peer-reviewed papers and reviews and one book chapters.

PhD Students

Kuan Pern Tan (Singapore)
I am currently graduate student in School and Computer Engineering (NTU Singapore) and Bioinformatics Institute (A*STAR Singapore). My research interest is with the modeling of protein 3D structure, as well as prediction/design of their biological functions.

Research Interests: The broad aim of my current work is the characterization of protein environments. Several biological utilities derived from my research include protein small molecule binding site prediction, design of temperature-sensitive mutant of protein, characterization of protein hydrogen bond and prediction of the mutational effect on protein functions. ‚Äč

Neelesh Soni
Neelesh Soni completed his BS-MS dual degree (Interdiciplinary Science) from IISER, Pune. He pursued his final year research project on structure determination of Intermediate Filament in our lab at BII, Singapore in 2012. Subsequently, he joined our Lab at IISER Pune as a Research Fellow in 2013, continuing the modeling of keratin structure. He is interested in developing tools to solve biological problems using mathematical and computational geometric approaches. Some of the tools developed by him are Disctransformation, Cell_list, CoulombPP, MVCG that are currently been used in the lab extensively.

Research Interests:
Currently, he is working on multiple research projects such as Keratin filament structure prediction, Protein-Ligand binding, Sumoylation Database Server (available locally at:, Click ( Apart from coding, he loves playing chess and riding bike.

Binh Thanh Nguyen (Singapore)
I am currently graduate student in Department of Biological Sciences (NUS Singapore) and Bioinformatics Institute (A*STAR Singapore).

Research Interests: My research interest is studying the protein-peptide interaction. Particularly, I am interested in the polyproline type II helices of peptide and its receptor.

Neeladri Sen

Hey, This is Neeladri Sen, an Int PhD Student who joined the lab for pursuing PhD in December 2014. Completed my Bachelors of Science(Microbiology) from St. Xavier's, Kolkata in 2012.
Other than this, in free time I can keep myself glued to T.V./Laptop watching cartoons,movies or shows. In addition, I have some interest in painting too.

Research Interests: I am presently working on designing tools for predicting the residue depth of proteins from the primary sequence. Residue depth has been associated with various important properties like pKa, ligand binding site, temperature sensitive mutation etc. We also plan to use depth to get to the 3D structure of proteins, which is a long time goal. Another aspect that I started looking recently is designing interaction interfaces between proteins. This might further lead to designing vaccines,ligand interfaces etc.

Yogendra Ramtirtha
Hey, this is Yogendra Ramtirtha (yogi). I joined IISER-Pune (and the lab) as a Ph.D. student in August, 2014. I did my Integrated M.Sc. Biotechnology from Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University (SPPU).

Research Interests: I am interested in studying micro-environment of amino acid residues in protein structures that undergo post-translational modfications and also to study how do these modifications bring about changes in interactions between different proteins. In my free time, I like to go out on a trip, read some articles related to history, watching movies and listening to music.

Sanjana Nair
Past: Bachelor of Science in Microbiology (Mumbai University)
Current: Integrated PhD Student 2nd Year

Research Interests:
Currently my focus is on the interactions between protein and specific DNA regions. The methods by which the proteins recognize DNA are varied and the major rules which need to be followed by a DNA-binding protein need to be discovered. For this purpose, double stranded DNA-protein complexes need to be analysed. The region of interest is the one which is bound in both the macromolecules.
If the protein binds to the predicted sequence, we have the proof of principle. The application for such a discovery of rules would be that a protein can be engineered to bind a region of DNA strongly. This strong binding can influence the transcription of the gene in question and thus induce gene silencing. If this method is used in combination with miRNA silencing, it could completely inhibit formation of the protein. It can also be modified to be temperature sensitive and therefore allow us to study lethal mutations.

Lab Rotational Students

Srinivasa Sasank Konakamchi
Research Interests: I'm an integrated PhD student of the 2015 batch. Before joining Madhu's lab, I rotated in Dr. Nixon Abraham's lab, working on olfaction in mice. My interest lies in computational and experimental neuroscience.

5th year project students

Akash Bahai
I joined the lab in February 2015 for my master thesis project.

Research Interests:
I am currently working on developing a statistical potential based on chemical groups to assess homology models. I recently completed my BS-MS degree from IISER, Pune in December 2015.

Ankit Roy
I am a 5th year integrated MSc student of Institute of Bioinformatics and Biotechnology (IBB), Pune.

Research Interests:
I am interested in Cell and Molecular Biology with a keen interest in Computational Biology and Data Analysis. My earlier projects include, cloning and over expression of an anti-microbial peptide from Bacillus licheniformis to Escherichia coli BL21-AI. Currently I am working on a project which aims to model the 3D structures of the complete proteome of Plutella xylostella.

Summer Project Students

Mohammed Aamir

Ashley Sreejan

Informal Students

Nida farheen
Sukanya Pandey
Vishrut Patel
Rahul Iyer